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Manually remove certain region in multiple sequence alignment


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#1 dcch

dcch

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Posted 31 October 2012 - 10:53 PM

Hello.

I have constructed a MSA, but I observed that certain part in the alignment has a large gaps due to the presence of unconserved region of a protein. I wish to remove that part of the protein by replacing those unconserved region with symbol // . Is there any tool with such function? Currently I am using GeneDoc, but the sequence location indicator automatically substracted when I removed that region in residue edit mode. Is this normal for a MSA? I thought the sequence location indicator should remain same (or increase due to participation of remaining sequence) even if I removed that region.

Thanks!

Edited by dcch, 31 October 2012 - 11:20 PM.





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